Markers + reference

Primula

103 species · Primulaceae · Ericales

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Species 103
Genome length 150–155 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 421 0.1279 0.90 72.3 yes View details
trnK-UUU-rps16 LSC 810 0.0816 0.95 80.7 yes View details
rps16-trnQ-UUG LSC 713 0.0884 0.99 84.1 yes View details
trnS-GCU-trnG-UCC LSC 604 0.0758 0.98 83.2 yes View details
rpoB-trnC-GCA LSC 1035 0.0678 0.99 83.5 yes View details
psbM-trnD-GUC LSC 1112 0.0775 0.99 81.9 yes View details
petA-psbJ LSC 1011 0.0738 1.00 83.7 yes View details
psbE-petL LSC 1201 0.0678 0.96 81.4 yes View details
ndhF-rpl32 SSC 861 0.0792 0.99 82.1 yes View details
ycf1 SSC 5466 0.0556 0.99 78.6 yes View details
trnE-UUC-trnT-GGU LSC 643 0.0681 0.98 86.6 yes View details
trnT-GGU-psbD LSC 1264 0.0621 0.99 84.8 yes View details
matK LSC 1533 0.0524 1.00 84.5 yes View details
rbcL-accD LSC 620 0.0526 0.99 84.5 yes View details
atpH-atpI LSC 730 0.0637 1.00 83.0 yes View details
rps16 LSC 1076 0.0492 1.00 82.9 yes View details
pafI-trnS-GGA LSC 859 0.0658 0.98 82.9 yes View details
trnF-GAA-ndhJ LSC 582 0.0701 0.98 82.6 yes View details
trnT-UGU-trnL-UAA LSC 795 0.0600 0.97 82.4 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CTGCGACTGCTGTTTTCTTG 794–1102 0.981 89.9
trnH-GUG-psbA_p2 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CTGCGATTGAAGCTCCATCT 345–563 0.495 70.7
trnH-GUG-psbA_p3 trnH-GUG-psbA TTAGTTATGGGCGAACGACG GGTGTAGCTGGTGTATTCGG 775–993 0.495 70.6
trnH-GUG-psbA_p4 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CTGCGACTGCTGTTTTCTTG 918–1136 0.485 70.5
trnH-GUG-psbA_p5 trnH-GUG-psbA TTAGTTATGGGCGAACGACG TTCCCTCTAGACCTAGCTGC 361–579 0.485 70.1
trnK-UUU_p1 trnK-UUU ATGCCCGTGTCAACCAATAC TGACAACAGTGCATCGAACA 2861–3000 0.447 65.1
trnK-UUU_p2 trnK-UUU CCCGTGTCAACCAATACCTA TGACAACAGTGCATCGAACA 2858–3000 0.524 64.0
trnK-UUU_p3 trnK-UUU ATATGCCCGTGTCAACCAAT TGACAACAGTGCATCGAACA 2863–3000 0.398 64.0
trnK-UUU_p4 trnK-UUU TGCCCGTGTCAACCAATAC TGACAACAGTGCATCGAACA 2860–3000 0.476 62.1
trnK-UUU_p5 trnK-UUU TATGCCCGTGTCAACCAATA TGACAACAGTGCATCGAACA 2862–3000 0.427 60.0
matK_p1 matK AGCAGCAATGAAGGCGATAA AAGACCACGACTGATCCTGA 2824–2892 0.951 89.1
matK_p2 matK AGCAGCAATGAAGGCGATAA AGACCACGACTGATCCTGAA 2823–2891 0.932 88.3
matK_p3 matK ACTCCCAAGCACACGAATTT AAGACCACGACTGATCCTGA 2633–2692 0.534 71.9
matK_p4 matK ACTCCCAAGCACACGAATTT AGACCACGACTGATCCTGAA 2632–2691 0.534 71.9
matK_p5 matK ACTCCCAAGCACACGAATTT GTGTGGGTGCGAGAAATACT 2360–2415 0.350 63.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CGAGATCTTCGGAAAGTGGG 859–1155 0.893 86.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT CGAGATCTTCGGAAAGTGGG 860–1156 0.893 86.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TTTGAATGAGCCGTACGAGG 983–1279 0.388 66.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT TTTGAATGAGCCGTACGAGG 984–1280 0.388 66.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTATTTCTCGCACCCACAC TTTGAATGAGCCGTACGAGG 1251–1519 0.311 63.6
rps16_p1 rps16 TGTTCGATGCACTGTTGTCA GAGGTTCGAATCCTTCCGTC 2091–2999 0.981 90.2
rps16_p2 rps16 TGTTCGATGCACTGTTGTCA AGTCTTCCCTCCCATCAGTC 1664–1957 0.456 68.8
rps16_p3 rps16 TGTTCGATGCACTGTTGTCA GTCTTCCCTCCCATCAGTCT 1663–1956 0.456 68.8
rps16_p4 rps16 TGTTCGATGCACTGTTGTCA AGGACTCAAGTCTTCCCTCC 1672–1965 0.350 65.1
rps16_p5 rps16 TGTTCGATGCACTGTTGTCA TCAAGTCTTCCCTCCCATCA 1667–1960 0.350 62.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 733–1506 0.990 91.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 726–1499 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 734–1507 0.981 87.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TTCGGAGGTTCGAATCCTTC 737–1510 0.990 86.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 730–1503 1.000 85.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (103)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Primula agleniana PV866628.1 152063 View on NCBI ↗
Primula algida NC_053582.1 154420 View on NCBI ↗
Primula alpicola NC_053588.1 154220 View on NCBI ↗
Primula ambita NC_058260.1 153837 View on NCBI ↗
Primula amethystina NC_053577.1 151565 View on NCBI ↗
Primula amethystina subsp. argutidens NC_065379.1 151560 View on NCBI ↗
Primula anisodora NC_053578.1 151674 View on NCBI ↗
Primula asarifolia NC_058256.1 153905 View on NCBI ↗
Primula atrodentata NC_053587.1 154713 View on NCBI ↗
Primula bathangensis PQ468696.1 153823 View on NCBI ↗
Primula beesiana NC_046770.1 150873 View on NCBI ↗
Primula blinii PQ468698.1 154510 View on NCBI ↗
Primula bracteata NC_053592.1 153439 View on NCBI ↗
Primula bulleyana NC_046947.1 150978 View on NCBI ↗
Primula calliantha subsp. bryophila ON804895.1 152055 View on NCBI ↗
Primula calyptrata NC_053606.1 153273 View on NCBI ↗
Primula capitata NC_053589.1 154663 View on NCBI ↗
Primula cavaleriei NC_088048.1 153063 View on NCBI ↗
Primula cawdoriana NC_053586.1 154376 View on NCBI ↗
Primula chionantha NC_053583.1 150974 View on NCBI ↗
Primula cicutariifolia NC_053605.1 151974 View on NCBI ↗
Primula daonensis PP541896.1 154234 View on NCBI ↗
Primula deflexa PQ468702.1 154554 View on NCBI ↗
Primula dejuniana PQ213817.1 152175 View on NCBI ↗
Primula densa NC_058262.1 153332 View on NCBI ↗
Primula denticulata subsp. sinodenticulata NC_050247.1 154660 View on NCBI ↗
Primula dickieana PQ468703.1 151754 View on NCBI ↗
Primula dryadifolia NC_053596.1 154181 View on NCBI ↗
Primula duclouxii NC_058263.1 153028 View on NCBI ↗
Primula dumicola NC_058257.1 153756 View on NCBI ↗
Primula effusa NC_058259.1 153056 View on NCBI ↗
Primula elatior subsp. intricata PP541898.1 153636 View on NCBI ↗
Primula erythrocarpa NC_053598.1 154590 View on NCBI ↗
Primula faberi NC_053576.1 151513 View on NCBI ↗
Primula farinosa PP541897.1 154656 View on NCBI ↗
Primula farinosa var. hannasanensis MZ779112.1 154772 View on NCBI ↗
Primula farinosa var. koreana MZ779113.1 154667 View on NCBI ↗
Primula farreriana PP842194.1 150962 View on NCBI ↗
Primula filchnerae NC_051972.1 151443 View on NCBI ↗
Primula fistulosa PQ412516.1 154368 View on NCBI ↗
Primula flaccida NC_053595.1 154752 View on NCBI ↗
Primula flava PQ536122.1 154347 View on NCBI ↗
Primula florindae NC_053579.1 154429 View on NCBI ↗
Primula forbesii NC_061696.1 152944 View on NCBI ↗
Primula gemmifera NC_053590.1 154650 View on NCBI ↗
Primula geraniifolia NC_053600.1 153979 View on NCBI ↗
Primula handeliana NC_039348.1 151081 View on NCBI ↗
Primula helodoxa NC_046771.1 151909 View on NCBI ↗
Primula heucherifolia NC_053580.1 153723 View on NCBI ↗
Primula hookeri NC_053593.1 151314 View on NCBI ↗
Primula hubeiensis NC_056372.1 151759 View on NCBI ↗
Primula jiugongshanensis NC_056335.1 151696 View on NCBI ↗
Primula knuthiana NC_039350.1 152502 View on NCBI ↗
Primula kwangtungensis NC_034371.1 153757 View on NCBI ↗
Primula kweichouensis NC_088047.1 154303 View on NCBI ↗
Primula mallophylla PQ310524.1 150733 View on NCBI ↗
Primula medogensis PP860589.1 151486 View on NCBI ↗
Primula meishanensis PQ213816.1 151988 View on NCBI ↗
Primula merrilliana NC_053604.1 151226 View on NCBI ↗
Primula obconica NC_046415.1 153694 View on NCBI ↗
Primula obconica subsp. begoniiformis MK344757.1 154068 View on NCBI ↗
Primula obconica subsp. fujianensis MK344734.1 154023 View on NCBI ↗
Primula obconica subsp. obconica OK040681.1 153861 View on NCBI ↗
Primula obconica subsp. parva MK344728.1 154057 View on NCBI ↗
Primula obconica subsp. werringtonensis OQ928035.1 154103 View on NCBI ↗
Primula ovalifolia NC_064961.1 151618 View on NCBI ↗
Primula partschiana NC_088045.1 153898 View on NCBI ↗
Primula pelargoniifolia PQ784118.1 153931 View on NCBI ↗
Primula pellucida NC_050248.1 153225 View on NCBI ↗
Primula poissonii NC_024543.1 151664 View on NCBI ↗
Primula polyneura PQ523385.1 153453 View on NCBI ↗
Primula pumilio NC_065465.1 154705 View on NCBI ↗
Primula purdomii NC_053591.1 151325 View on NCBI ↗
Primula qiandaoensis OQ053493.1 152035 View on NCBI ↗
Primula ranunculoides NC_056361.1 150187 View on NCBI ↗
Primula rubifolia NC_058261.1 154063 View on NCBI ↗
Primula saxatilis NC_053584.1 153053 View on NCBI ↗
Primula secundiflora NC_053585.1 151583 View on NCBI ↗
Primula sikkimensis NC_050243.1 150496 View on NCBI ↗
Primula sinensis NC_030609.1 150859 View on NCBI ↗
Primula sinolisteri var. aspera MK344744.1 153348 View on NCBI ↗
Primula sinolisteri var. sinolisteri MK344746.1 154091 View on NCBI ↗
Primula sinuata NC_088046.1 151752 View on NCBI ↗
Primula smithiana NC_061709.1 151811 View on NCBI ↗
Primula sonchifolia NC_053594.1 150974 View on NCBI ↗
Primula spectabilis PP541899.1 154253 View on NCBI ↗
Primula stenocalyx NC_058249.1 153678 View on NCBI ↗
Primula strumosa NC_053599.1 151897 View on NCBI ↗
Primula taliensis NC_053601.1 151233 View on NCBI ↗
Primula tibetica PX068033.1 153925 View on NCBI ↗
Primula tsiangii NC_046755.1 153281 View on NCBI ↗
Primula veris subsp. veris PP541900.1 153559 View on NCBI ↗
Primula vialii NC_065387.1 154897 View on NCBI ↗
Primula vilmoriniana NC_058258.1 154061 View on NCBI ↗
Primula virginis NC_053581.1 151163 View on NCBI ↗
Primula waltonii NC_058808.1 154124 View on NCBI ↗
Primula wannanensis NC_064960.1 151733 View on NCBI ↗
Primula wawushanica PQ568378.1 152999 View on NCBI ↗
Primula wilsonii MW442886.1 151677 View on NCBI ↗
Primula woodwardii NC_039349.1 151666 View on NCBI ↗
Primula x polyantha PP541901.1 153536 View on NCBI ↗
Primula xinningensis ON208990.1 151601 View on NCBI ↗
Primula zhengyii OQ928037.1 153416 View on NCBI ↗